networkWrapper: networkWrapper

In hemoshear/pathwayTalk:

networkWrapper

Description

Wrapper function for the pathwayTalk workflow.

Usage

networkWrapper(
  expression_matrix,
  groups,
  DEPs,
  pathways,
  pathway_alpha,
  lambda,
  ...
)

Arguments

expression_matrix	An matrix of gene expression data where the row names are the gene probe identifiers and column names are the sample identifiers. For RNAseq data, a matrix of un-normalized integer counts. For microarray data, a matrix of intensity values for gene probes with pre-processing completed, including normalization, removing control sequences, log2 transformation, and collapse to genes.
groups	A dataframe containing the sample identifiers ('sample_id', a factor with the reference condition as the first level) and associated treatment conditions ('group'). The sample identifiers must be in the same order as the columns of the count_matrix.
DEPs	A dataframe of pathways with associated p-values in a column 'p'. The output of pathwayEnrichment().
pathways	A list in which each element is a named list of genes corresponding to a particular pathway.
pathway_alpha	Significance level for enriched pathways. Pathways with a Fisher's exact test p-value less than 'pathway_alpha' will be labeled as enriched for the purposes of downstream analyses.
...	Additional arguments to crosstalkNetwork() function.

Value

Returns a named list.

• full_network - An igraph object representing the full network of top-performing pathway pairs.

• full_network_results - A dataframe describing the full network.

• pruned_network - An igraph object representing the pruned network of top-performing pathway pairs.

• pruned_network_results - A dataframe describing the pruned network.

hemoshear/pathwayTalk documentation built on July 16, 2022, 12:09 a.m.